Search Results (560)

Topmouth culter (Culter alburnus) is one of the most economically important freshwater fish in China, but intensive aquaculture has caused germplasm degradation and reduced growth performance, while the genetic basis underlying growth variation in this species remains poorly understood. This study aimed to identify major-effect loci and candidate genes associated with growth-related traits to support molecular breeding. Whole-genome resequencing (average depth 11.44×) was performed on 300 individuals derived from random mating among three geographic populations (Danjiangkou, Taihu, and Poyang Lake); 239 individuals with complete phenotypic records were retained for a genome-wide association study (GWAS) of five growth-related traits, including body weight (BW), body weight without viscera (BWW), total length (TL), body length (BL), and body height (BH). After stringent filtering, 7,597,008 high-quality single-nucleotide polymorphisms (SNPs) were obtained, and association analysis was conducted using a linear mixed model, followed by Benjamini–Hochberg false discovery rate correction and 1000-permutation testing for BW and BL. Six genome-wide significant SNPs and 473 suggestive SNPs were identified, with individual significant SNPs explaining over 11% of phenotypic variance, indicating candidate loci of putatively moderate-to-large effect. Significant SNPs were predominantly clustered on chromosomes 16 and 19. Four candidate genes—aig1, cacna1b, pgm5, and bcr—were identified, with functions related to lipid metabolism, muscle structure, and cell proliferation. This first population-level GWAS in topmouth culter provides valuable molecular markers for marker-assisted selection and lays a foundation for accelerated genetic improvement of this species. Full article

Soil salinity is a major constraint on global wheat productivity, yet the genetic and molecular determinants of root system architecture (RSA) adaptation under salt stress remain poorly characterized. We integrated a genome-wide association study (GWAS) of 566 wheat accessions with comparative RNA-seq transcriptomics to identify the genetic and transcriptional determinants of RSA adaptation under 200 mM NaCl. GWAS identified a candidate locus on chromosome 7B harboring TaIAO, which encodes a protein with predicted aldehyde oxidase-like activity consistent with a role in tryptophan-dependent auxin biosynthesis. Accessions carrying the favorable CC allele exhibited significantly greater root volume retention than those carrying the GG genotype (p < 0.001). Comparative RNA-seq revealed that the salt-tolerant Sarajevo 1 exhibited coordinated transcriptional repression of three distinct modules—cell wall expansion (TaExpansin), auxin redistribution (TaPIN-like), and stress-associated ROS defense (TaPOD1)—whereas the sensitive genotype CI 17260 aberrantly induced or incompletely repressed these modules under stress. ELISA-based IAA quantification, ROS imaging, and qRT-PCR analysis provided independent physiological and transcriptional support for these patterns. These findings support a two-tier adaptive model in which constitutive genetic variation at the TaIAO locus may contribute to a developmental baseline, coupled with coordinated stress-responsive transcriptional repression of energy-consuming modules, providing promising targets for marker-assisted breeding of salt-tolerant wheat. Full article

The translocation of sucrose into spike grains during the grain-filling stage directly affects rice yield and quality. The sugar transporters OsSWEET11 and OsSWEET15 are key sucrose transporters essential for rice (Oryza sativa L.) grain filling. To elucidate their effects on grain traits, we analyzed sequence polymorphisms of these two genes in 139 landrace rice varieties from Yunnan, China, and conducted association and haplotype analyses. Our results indicated that grain filling degree was closely associated with grain shape, where wider grains negatively impacted grain plumpness. The association analysis revealed eight significant SNPs: six located in the coding region of OsSWEET15 that influenced grain length, thickness, density, and 1000-grain weight (TGW), while two SNPs in OsSWEET11 affected TGW and the thickness of milled rice grains. Haplotype analysis further validated these trait associations: OsSWEET15 Hap2 and Hap3 conferred longer grains (with Hap2 additionally increasing TGW and Hap3 enhancing grain density/plumpness), whereas Hap1 produced narrower and thicker grains. Consistently, OsSWEET11 Hap2 was also linked to higher TGW. The superior haplotypes identified here deepen our understanding of the genetic basis of rice grain filling and serve as potential molecular markers for marker-assisted rice breeding. Full article

Tomato (Solanum lycopersicum L.) is a globally important vegetable crop and a major dietary source of bioactive compounds, including lycopene, ascorbic acid, phenolics, and minerals. Modern tomato breeding has substantially improved yield, uniformity, and postharvest performance; however, these gains have often been accompanied by reduced flavor quality, lower nutritional value, and narrowing of the genetic base. This review synthesizes available evidence on Lithuanian tomato germplasm and evaluates its relevance for future breeding strategies aimed at enhancing genetic gain under Northern European conditions. The review integrates published data on genetic diversity, molecular characterization, morphological traits, fruit quality parameters, and yield performance of Lithuanian cultivars and hybrids developed in Lithuania. SSR-based studies indicate moderate genetic diversity, with mean expected heterozygosity of approximately 0.51 and mean PIC values of 0.47 in cultivars and 0.45 in hybrids, while also confirming a relatively narrow breeding pool. Lithuanian cultivars display substantial variation in fruit morphology, dry matter, soluble solids, firmness, lycopene, ascorbic acid, and yield. Traditional cultivars such as ‘Svara’, ‘Milžinai’, ‘Slapukai’, and ‘Balčiai’ show valuable nutritional and technological traits, whereas hybrids such as ‘Auksiai H’, ‘Adas H’, and ‘Ainiai H’ demonstrate improved productivity and firmness. The available evidence suggests persistent yield–quality trade-offs, particularly between productivity, soluble solids content, antioxidant accumulation, and postharvest performance. Although Lithuanian germplasm does not represent exceptionally broad genetic diversity, it contains regionally adapted material with stabilized trait combinations useful for breeding resilience, nutritional quality, and adaptation to temperate environments. Future progress will require broadening the genetic base and integrating traditional breeding with marker-assisted selection, genomic selection, GWAS, genome editing, multi-omics, and pangenomic approaches. Overall, Lithuanian tomato germplasm represents a locally adapted regional resource for translating genetic diversity into genetic gain in modern tomato breeding. Full article

Wheat powdery mildew and stripe rust, caused by Blumeria graminis f. sp. tritici (Bgt) and Puccinia striiformis f. sp. tritici (Pst), respectively, are two devastating diseases that threaten global wheat production. Long-term reliance on a limited number of resistance genes can accelerate resistance breakdown. Triticum urartu (2n = 14, A^uA^u), the progenitor of the wheat A subgenome, serves as a valuable gene pool for disease resistance. In this study, we identified three T. urartu accessions exhibiting high resistance to Bgt and Pst. Molecular marker analysis indicated that PI 428215 and PI 428315 carry Pm60b, whereas CITR 17664 carries both Pm60 and YrU1. Durum–T. urartu amphiploids (AABBA^uA^u) displayed resistance responses identical to their T. urartu parent and were used as bridges to transfer these resistance genes into a common wheat (AABBDD) background. Using marker-assisted selection (MAS), recurrent backcrossing, selfing, and phenotypic screening, we developed wheat lines carrying Pm60, Pm60b, YrU1, or Pm60 + YrU1. Segregation analysis in backcross-derived populations supported the functionality of these genes in the common wheat background. The selected introgression lines have high resistance to Bgt and Pst and showed no obvious adverse agronomic effects, providing useful germplasm for wheat disease resistance breeding. This study used a “multi-resistance, multi-combination” pyramiding strategy by MAS to introduce resistance genes from wild wheat into common wheat. Full article

Pumpkin (Cucurbita spp.) is a globally significant vegetable crop known for its high nutritional value and remarkable phenotypic diversity. Yet, the surge in new cultivar releases has overwhelmed traditional morphological descriptors, creating critical gaps in variety purity control and breeders’ rights enforcement. Despite the established utility of SNP markers as the gold standard for genetic analysis, a dedicated high-resolution molecular database for modern pumpkin cultivars remains unavailable. To address this gap, we conducted whole-genome resequencing (WGS) on 94 representative pumpkin cultivars (spanning C. moschata, C. maxima, and C. pepo). Clean reads were mapped to the Cucurbita maxima reference genome. We employed a stringent pipeline to identify genomic variants and utilized STRUCTURE software, Principal Component Analysis (PCA), and Neighbor-Joining (NJ) trees to evaluate population stratification. Linkage disequilibrium (LD) decay and DNA fingerprinting barcodes were also developed. A total of 8,873,150 high-quality variants were identified, including 7,345,007 SNPs and 1,528,143 InDels, with an average SNP density of 21,281.50 SNPs/Mb. Population analysis consistently categorized the 94 cultivars into two primary subpopulations (G1 and G2). The first two PCs accounted for 74.06% of the total genetic variance. Further analysis revealed that G1 possessed a more complex genetic architecture and slower LD decay compared to G2, suggesting distinct selection histories. Finally, we screened for highly informative biallelic SNPs to construct a DNA fingerprinting database, enabling precise sample discrimination through unique chromatic barcodes. This study fills a critical gap in pumpkin genomics by establishing a high-density SNP database and a robust fingerprinting system. These resources provide a definitive tool for variety certification, seed purity testing, and the advancement of molecular-assisted breeding in pumpkin. Full article

Drought stress is the most pervasive abiotic constraint on global crop productivity, with projected intensification under climate change threatening the yields of staple crops including wheat, rice, maize, and legumes. Conventional breeding approaches have delivered limited gains against drought tolerance, constrained by the polygenic and multifactorial nature of stress adaptation, the complexity of genotype-by-environment interactions, and the inadequacy of field-based phenotyping under variable stress conditions. Omics technologies, including genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics, have substantially advanced the molecular dissection of drought tolerance by enabling high-resolution characterization of stress-responsive genes, regulatory networks, adaptive proteins, and metabolic reprogramming pathways. Specific traits targeted include root system architecture and depth, osmotic adjustment capacity through proline and glycine betaine accumulation, antioxidant defense mechanisms, ABA-mediated stomatal regulation, LEA protein accumulation, epigenetic stress memory, and yield stability under water deficit. This review systematically examines omics-based strategies for drought stress mitigation across major crops, highlighting individual omics contributions, multi-omics integration frameworks, computational tools including machine learning and AI-driven predictive modelling, and translational breeding applications. Case studies in wheat, rice, maize, and legumes illustrate how omics-driven approaches accelerate precision breeding for drought resilience through marker-assisted selection, genomic selection, and CRISPR-based gene editing. Challenges including data integration complexity, high implementation costs, limited cross-species transferability, and the need for field-scale validation of microbiome-based strategies are critically addressed. Future perspectives encompassing single-cell and spatial omics, AI-driven predictive breeding, digital agriculture integration, and international data governance frameworks are discussed. By aligning with climate-smart agriculture principles, multi-omics approaches provide a robust and transformative foundation for developing drought-resilient crop cultivars suitable for water-limited production systems worldwide. Full article

Phosphoglycerate kinase (PGK) is a vital glycolytic enzyme that provides energy and carbon skeletons to support fatty acid synthesis. However, the PGK gene family has not been characterized in soybean (Glycine max), and its role in soybean oil accumulation remains unclear. Here, we identified six GmPGK genes in soybean, all of which encode proteins containing conserved PGK domains. Phylogenetic analysis clustered soybean PGK proteins into three groups. Analysis of GmPGK promoters revealed relatively abundant cis-elements related to plant growth, development, and phytohormone response. Expression profiling showed that GmPGK5 transcript abundance increases progressively with oil accumulation during seed development, and is significantly higher in the high-oil variety NN1138-2. Overexpression of GmPGK5 significantly increased total fatty acid content in soybean hairy roots. A single nucleotide polymorphism (SNP) located at Chr15:49447855 within the GmPGK5 promoter was significantly associated with both seed oil content and seed weight in natural soybean accessions. Based on this SNP, a derived cleaved amplified polymorphic sequence (dCAPS) marker was developed to facilitate soybean molecular breeding. Our findings suggest that GmPGK5 may positively regulate fatty acid accumulation in soybean. The identified natural variation and dCAPS marker provide potential valuable tools for marker-assisted selection to improve soybean oil content and seed weight. Full article

Maize (Zea mays L.) is one of the most important cereal crops worldwide, with yield being a complex quantitative trait controlled by multiple genetic factors. The aim of this study was to identify molecular markers associated with maize yield using next-generation sequencing (NGS), association mapping, and physical mapping approaches. A total of 122 maize hybrids were evaluated under field conditions in a randomized complete block design with three replications. Phenotypic data were collected for grain yield, while genotypic data were obtained using DArTseq technology, resulting in the identification of 60,436 SilicoDArT and 32,178 SNP markers. After quality filtering, 25,078 markers were used for further analyses. Analysis of variance revealed statistically significant differences among hybrids in terms of yield (p < 0.001), with values ranging from 12.67 to 18.52 kg/10 m². Genetic similarity among hybrids ranged from 0.434 to 0.957, indicating substantial genetic diversity. Cluster analyses based on phenotypic and genotypic data showed a lack of correspondence between yield performance and genetic similarity. Genome-wide association studies (GWAS) identified 2478 markers significantly associated with yield, including 47 highly significant markers (Logarithm of the Odds − LOD > 4.0). Individual markers explained between 2.4% and 18.7% of yield variation. Ten markers with the highest contribution to yield variability (13.30–18.70%) were selected as the most promising candidates for further breeding applications. These markers represent promising candidates for marker-assisted selection and genomic selection (GS) of high-yielding maize genotypes. These are some of the first positive results. The integration of phenotypic evaluation with high-throughput genotyping and association mapping provides valuable insights into the genetic architecture of yield and offers practical tools for the development of high-yielding maize cultivars. Full article

Plant diseases remain a major constraint to crop productivity and global food security. Conventional breeding has long been used to develop resistant cultivars through the introgression of resistance traits from wild relatives and the selection of favorable phenotypes. However, this process is often slow and limited by linkage drag, known genetic diversity, intrinsic genetic limitations, and the rapid evolution of pathogen populations. Molecular breeding strategies, including marker-assisted selection and genomic selection, have improved the precision of resistance breeding but still rely on existing genetic variation. Recent advances in genome editing technologies are transforming plant breeding by enabling precise modification of gene targets. CRISPR-based systems allow targeted gene knockouts, promoter editing, allelic replacement, and multiplex editing to rapidly generate resistance traits. Many studies have demonstrated that editing susceptibility genes or regulatory regions can enhance resistance to diverse pathogens. Recent research shows that resistance can also be improved by targeting non-classical genes involved in plant immunity, including transcription factors, membrane transporters, heat shock proteins, cell wall-related genes, metabolic enzymes, and epigenetic regulators. Emerging tools such as base editing, prime editing, regulatory tools, and transposon-associated genome engineering systems are further expanding the precision and versatility of plant genome editing. Despite these advances, challenges related to delivery systems, editing efficiency, regulatory frameworks, and field validation remain. Continued technological progress and improved knowledge of plant immune networks will be essential to fully integrate genome editing into crop improvement programs. Full article

Sweetpotato (Ipomoea batatas (L.) Lam.) is an important multifunctional crop with great value in food supply, industrial processing and bioenergy utilization. Crude protein content (CPC) is a core target trait for sweetpotato quality breeding. To dissect the genetic basis of CPC and identify key candidate genes, we used an F₁ population of 212 individuals. CPC was measured by near-infrared reflectance spectroscopy (NIRS) in 2020 and 2021, and QTL mapping was performed using a high-density SNP genetic linkage map. Candidate genes were explored via a genome-wide association study (GWAS), multiple-database functional annotation, and quantitative real-time PCR (qPCR) validation. The results showed that: (1) CPC in the population exhibited a continuous normal distribution with high inter-year stability, and phenotypic variation was mainly controlled by genetic factors; (2) one stable minor-effect QTL for CPC, qCPC09-1, was mapped to Chr09: 7906895–8614924 bp, explaining 5.7% of phenotypic variation; (3) GWAS detected no significant SNP loci, suggesting that CPC is regulated by multiple minor-effect genes; (4) genes within the qCPC09-1 interval were significantly enriched in three protein synthesis-related KEGG pathways: ribosome, nitrogen metabolism and ubiquinone and other terpenoid–quinone biosynthesis; (5) qPCR verified that itf09g13420 and itf09g13230 were upregulated in the low-CPC parent Yushu 10 and negatively correlated with CPC, while itf09g13550 was upregulated in the high-CPC parent Xin 24 and positively correlated with CPC. These three genes exhibited expression patterns highly consistent with phenotypic differences. This study provides a theoretical basis and technical support for molecular marker-assisted breeding and elite germplasm innovation in sweetpotato. Full article

Background: Long non-coding RNAs (lncRNAs) are increasingly recognized as key regulators of gene expression, playing pivotal roles in diverse biological processes, including reproduction. This study identified and characterized lncRNAs located near fertility-associated genes in Retinta beef cattle, exploring their potential regulatory roles via DNA–RNA triplex formation using in silico approaches. Methods: We applied an integrative bioinformatics pipeline to identify potential triplex interactions, predicting structurally accessible regions within the lncRNAs and demonstrating the statistical enrichment of binding sites across known regulatory genomic elements. Results: Twelve protein-coding genes previously linked to female fertility or male scrotal circumference were analyzed, revealing 16 unique lncRNAs within ±50 kb windows, predominantly on BTA5. We predicted high-confidence triplex-forming oligonucleotides (TFOs) for most gene-lncRNA pairs. Our results suggest robustness and sequence specificity, as interactions were disrupted by sequence permutation or when a control background sequence was used. RNA secondary-structure analysis revealed that TFOs generally lie in exposed regions, supporting their accessibility for triplex formation. Furthermore, promoter and regulatory regions of fertility-associated genes were enriched in predicted triplex target sites (TTSs), with some overlapping CpG islands and enhancer regions, leading to the hypothesis that these lncRNAs might play a role in epigenetic regulation. Conclusions: Overall, these findings establish computationally derived hypotheses regarding the potential molecular mechanisms by which lncRNAs may modulate reproductive efficiency in cattle and highlight specific lncRNAs as promising targets for functional studies and marker-assisted breeding. Full article

Ramie (Boehmeria nivea) is renowned for its superior fiber strength, length, and unique properties, yet its genetic improvement has lagged behind other fiber crops. This review synthesizes recent advances in ramie fiber development at the genetic, genomic, and molecular levels. Population genomic analyses have uncovered distinct domestication, improvement, and feralization signatures, identifying numerous fiber-related genes under selection. Parallel genetic and molecular studies have mapped scores of loci and genes governing fiber formation, laying the foundation for molecular breeding. However, despite the availability of genetic transformation systems, the need for methodological improvements remains a major challenge for engineering fiber traits via transgenic approaches. Overall, a solid research foundation has been established. Future progress in establishing marker-assisted and genomic selection breeding systems, optimizing transformation protocols, and developing efficient gene-editing methods holds promise for realizing molecular breeding to enhance fiber quality and yield in ramie. Full article

Pea (Pisum sativum L.) is an important temperate grain legume crop of high nutritional and agronomic value. Ascochyta blight, caused by a multi-species complex of necrotrophic fungi, remains a major constraint for pea production worldwide. This review synthesizes the available genetic, physiological and molecular knowledge on the pea–Ascochyta blight pathosystem, with emphasis on the genetic architecture of resistance, host defense mechanisms and the recent contributions from the omics disciplines. Current evidence indicates that genetic resistance to the various Ascochyta blight pathogens is incomplete and multicomponent, being associated with loci of small to moderate effect, with expression depending on organ, developmental stage and environment. Under field conditions, the observed phenotypes reflect the interaction between physiological resistance, plant architecture, phenology, canopy microenvironment and epidemic dynamics. Together, these factors bias phenotyping and limit the transferability of molecular markers. The practical value of these markers for use in marker-assisted selection (MAS) and genomic selection (GS) is presented and critically discussed. Future progress in breeding for Ascochyta blight resistance will depend on integrating molecular knowledge with a careful definition of ideotypes, well-calibrated phenotyping and multi-environment validation. Full article

Background/Objectives: Fall armyworm (FAW) (Spodoptera frugiperda) is a major constraint to maize production in Sub-Saharan Africa, including Mozambique. This study aimed to evaluate maize genotypes for resistance to FAW under greenhouse and field conditions and to assess the association between phenotypic resistance and genomic variation based on single nucleotide polymorphisms (SNPs). Methods: A total of 20 maize genotypes from the Agricultural Research Institute of Mozambique (IIAM) and the International Maize and Wheat Improvement Center (CIMMYT) were evaluated. FAW damage was quantified using the area under the damage progress curve (AUDPC). Phenotypic data were analyzed using ANOVA and mixed models, while molecular analysis was conducted using 10,603 SNP markers located on chromosomes previously associated with FAW resistance. Results: Significant genotypic differences were observed under greenhouse conditions (F = 1.94, p = 0.012) and in the field (p = 0.021), although environmental factors reduced variation in the field. Genotypes such as CML67, CML338, and Kenya amarelo (Acc3550) exhibited consistently lower AUDPC values across environments, indicating stable resistance. However, SNP allele proportion was not significantly associated with phenotypic resistance (r = 0.34, p = 0.147), and regression and ANOVA analyses confirmed the absence of a significant relationship (p > 0.05). Conclusions: FAW resistance in maize is quantitatively inherited and not explained by general genomic variation across candidate regions. Phenotypic screening remains essential, and further studies are required to identify specific loci for effective marker-assisted selection. The identified stable genotypes represent valuable resources for breeding FAW-resistant maize adapted to Mozambique. Full article